75N97019R00010_AV_Statement_of_Work_5.22.19.pdf

FINAL 75N97019R00010AV

STATEMENT OF WORK 1

TITLE: Chemical Structure and Data Support and Maintenance for NLM Web Applications (ChemIDplus)

STATEMENT OF WORK

(Dated 05/22/2019)

A. BACKGROUND INFORMATION

The ChemIDplus database is a public web-based search system that provides access to structure and nomenclature to identify chemicals cited in the National Library of Medicine (NLM) databases and in other major government databases. The database contains over 420,000 chemical records of which over 335,000 include chemical structures.

The Software/server/database used by ChemIDplus includes AccelrysHost, AccelrysDirect, BIOVIA, Linux server, Tomcat, Apache server and Oracle database. The software setup between these systems is complex, and needs to be monitored and upgraded with increased usage. The ChemIDplus system also provides the backend for the NLM Drug Information Portal and the Food and Drug Administration Substance Registry System (FDASRS). The Drug Information Portal provides users with links and selected drug information from NLM and other key U.S.

government agencies. The FDASRS which provides unique identifiers for substances in drugs, biologics, and more also provides links to additional resources. The data these systems generate and support must be updated, maintained and mined in order to provide optimal access and usability to the public.

This project involves significant amount of computer programming services, from data parsing, data transforming, to data mapping, for fulfilling data update on ChemIDplus from many other chemical, biomedical resources at NLM and on the Internet. It also involves developing stored procedures to implement business rules and quality control. This is an example of applying programming in a knowledge domain such as chemistry to improve data quality and the efficiency of data collection. The number of new records per month for ChemIDplus database is in the range of tens to hundreds. The number of new data lines is in the range of thousands to tens of thousands. Several thousand molecules are added to ChemIDplus database per year.

B. PURPOSE AND OBJECTIVE OF THE PROCUREMENT

The purpose of this procurement is to procure professional services to provide support and maintenance of ChemIDplus and related databases and applications. The objective is to add new chemicals, maintain data quality, expand the coverage of chemical structures, and achieve accuracy and consistency of the chemical structures.

C. CONTRACT REQUIREMENTS

Services may include but are not limited to the following:

STATEMENT OF WORK 2

1. Update ChemIDplus Data Elements - The contractor will update data elements within ChemIDplus such as the locators within the records. Locator examples include, but are not limited to: MeSH, Clinical Trials, and DailyMed.

2. Acquire Chemical Data and Draw Chemical Structures - The contractor will provide

NLM with structural diagrams in Accelrys format for chemicals in ChemIDplus that do not have structural data and/or for chemicals added to the database. NLM will prioritize this list according to need. Structures will either be drawn using programs such as AccelrysDraw, or converted using appropriate software from nomenclature in ChemIDplus.

3. Perform Quality Control on the ChemIDplus database - The contractor will systematically check all structure, name and molecular formula data for consistency and accuracy.

4. Acquire Drug Information - The contractor will monitor the monthly United States

Adopted Names (USAN) list, and by formatting data received under license from United States Pharmacopeia (USP) for addition to ChemIDplus. Also, update Locators such as Toxic Substances Control Act Chemical Substance Inventory (TSCAINV) when new data is available.

5. Additional Data Support – The contractor will provide additional data support for related database activities for interagency agreements or special enhancement activities related to ChemIDplus and related databases. Additional support activities are similar in nature to tasks 1-4. The contractor will attend bi-weekly team meetings remotely.

D. LABOR CATEGORIES AND LABOR HOURS

The government estimated that the following labor categories and total labor hours will be needed from the Contractor to perform the required services. The following is a sample of labor categories, labor hours and experience levels that would be appropriate for performance of this requirement. The vendor may propose other labor categories, labor hours and experience levels, if they would contribute to a more efficient solution; however, the vendor must demonstrate that the proposed personnel, labor hours and experience levels meet the Government’s requirement.

LABOR HOURS (Estimated, Not to Exceed)

Categories Base Period (10 months, 7/1/2019- 4/30/2020)

Option Period 1 (12 months, 5/1/2020- 4/30/2021)

Option Period 2 (12 months, 5/1/2021- 4/30/2022)

Estimated 3-Year

TOTAL

Base Effort Project Manager 100 120 120 340 Programmer 1,360 1,600 1,575 4,535 Chemist 280 300 300 880 Total Base Effort 1,740 2,020 1,995 5,755

STATEMENT OF WORK 3

Optional Effort Project Manager 8 8 8 24 Programmer 100 100 100 300 Chemist 0 0 0 0 Total Optional Effort 108 108 108 324

Total Labor Hours (Estimated, Not to Exceed)

1,848 2,128 2,103 6,079

1. Project Manager The project manager is responsible for managing project activities, deliverables, budget, and reporting.

Graduate degree in a related science, experience with large-scale biological and chemical information databases is required for this position.

2. Programmer The duties for the programmer are data maintenance and mining. There are no requirements on languages or technologies that the contractor chooses to do data parsing or data manipulation.

For example, SQL and PL/SQL are currently widely used in mining/querying/updating, as long as they are compatible with the deployed DBMS. It is advised for the programmer to access the live database remotely for up-to-date information. Holding a copy of the ChemIDPlus database for offsite work is not allowed.

Graduate degree, plus chemistry background, and experience with xml, script language, Tomcat, Apache, and Oracle databases are required for the programmer position.

3. Chemist The duties for the chemist are chemical structure data entry, drawing, and editing. The chemist will provide new structures in SDF (structure-data file) and new data following predefined data loading format.

Graduate degree in Chemistry, experience with MDL AccelrysHost, AccelrysDirect, and Oracle are required for the chemist position.

The contractor, with NLM approval, will determine what level of expertise is necessary for particular data tasks. For example, a junior or senior level programmer or chemist may be utilized depending on the specific needs related to completing individual task(s).

The Base Period of Performance will be 10 months from effective date of award with two 12-month option years, if exercised.

STATEMENT OF WORK 4

E. GOVERNMENT RESPONSIBILITIES

The NLM Contracting Officer's Representative (COR) will provide tasks and assign their relative priority. NLM will provide remote secure access to ChemIDplus and related databases, file maintenance programs and any NLM servers as needed to complete tasks.

F. REPORTING REQUIREMENTS INVOICING AND DELIVERABLES

Hours required for each task will be estimated after assignment by NLM, and hours will be reported after completion. The number of structures drawn for a given set of hours will also be tabulated. Monthly reports describing task activities and invoices should be submitted electronically to Contracting Officer's Representative (COR) email account. The Contractor shall notify NLM will be notified when 80% of the funds allocated have been spent.

G. INSPECTION AND ACCEPTANCE REQUIREMENTS

The NLM Contracting Officer's Representative (COR) will assign tasks, and work will be reviewed for completeness and efficacy.

H. TRAVEL

All meetings will be conducted remotely, therefore no travel is anticipated.

LABOR HOURS (Estimated, Not to Exceed)